bio-alignment-msa-parsing skillA
bio-alignment-msa-parsing is agent-read markdown (skill) from pku-yuangroup/openai4s: Parse and analyze multiple sequence alignments using Biopython. Extract sequences, identify conserved regions, analyze gaps, work with annotations, and manipulate alignment data for downstream analysis. Use when parsing or manipulating multiple sequence alignments..
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What the file says
## Version Compatibility Reference examples tested with: BioPython 1.83+, numpy 1.26+ Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # MSA Parsing and Analysis Parse multiple sequence alignments to extract information, analyze content, and prepare for downstream analysis. ## Required Import **Goal:** Load modules for parsing, analyzing, and manipulating multiple sequence alignments. **Approach:** Import AlignIO for reading, Counter for column analysis, and alignment classes for constructing modified alignments. ```python from Bio import AlignIO from Bio.Align import MultipleSeqAlignment from Bio.SeqRecord import SeqRecord from Bio.Seq import Seq from collections import Counter import numpy as np import pandas as pd ``` Optional for streaming and Easel-based weighting: ```python import pyhmmer ``` ## Loading Alignments **Goal:** Read an MSA file and inspect its dimensions. …
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How to install
mdr add pku-yuangroup/openai4s/bio-alignment-msa-parsing@git:20260821.2d1b678mdr add pku-yuangroup/openai4s/bio-alignment-msa-parsing@sha256:c22de96eab32dd9dPin to a label to follow the author's releases, or to a sha256 to freeze the exact bytes forever. Either way the resolved hash is written to mdr.lock, and mdr install reproduces it on any machine.
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Source
pku-yuangroup/openai4s · 586 stars · license MIT · pushed 2026-09-23 · branch main
API
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